[EMBOSS] Standalone on MacOSX Panther success

[Brett Kaufman]

I have receive such fantastic and patient help from Tim Carver that I 
though I would submit experience back to the emboss boards.

standalone Jemboss EMBOSS-2.8.0 successfully installed:

All of this was done on 10.3.1 with the latest fink installed and 
working.  At the time, EMBOSS-2.8.0 wasn't available through fink, so 
it was downloaded and installed from command line.  To repeat my steps, 
you will need to be certain that libiconv, gd2, and libpng are current. 
Remember to run fink selfupdate and update all a time or two to be 
certain everything is completely there ;).

download emboss-2.8.0, and embassy components. Emboss will install in 
/usr/local, so I moved the downloaded folders to a new directory 
/usr/local/installers.  The original folder is needed after the 
install, so this make a permanent home for the EMBOSS-2.8.0 folder.  
gunzip and tar-xvf everything.

 >cd /usr/local/installers/EMBOSS-2.8.0/jemboss/utils
 >./install-jemboss-server.sh

The Java file for Panther is:
/System/Library/Frameworks/JavaVM.framework/Home

Accepting the default responses usually works, except for the png 
driver.  In this installation, use --with-pngdriver=/sw.

when prompted, move the decompressed embassy files to the new embassy 
folder in EMBOSS-2.8.0 within the installer.

when installation is finished, there a few things that are worth 
changing.

As panther uses bash, I used pico ~/.bashrc to make sure that I can run 
emboss  from any directory):
PATH=$PATH:/usr/local/emboss/bin

The runJemboss file needs to be modified; however, the prescribed 
modification on the web are for runJemboss.csh, which is from 
emboss-2.7.1, rather than runJemboss.sh, which you will be using.

 >cd /usr/local/emboss/share/EMBOSS/jemboss
 >pico runJemboss.sh

remove the # on DYLD_LIBRARY_PATH...

Keep an eye open for word wrap issues.  Should you have launch issues, 
try pico -w and look for disconnect text.

I added Jemboss to the X11 menu:
Applications -> Customize
Name= Jemboss
Command= /usr/local/emboss/share/EMBOSS/jemboss/runJemboss.sh
Shortcut=j
done

hitting command-j will launch the application if x11 is active.

Make sure to dl clustalw and install it in /usr/local/bin to get emma 
to work properly.

primer3: this is sort of ugly, but it works.
download primer3_0_9_test from the whitehead institute. gunzip and tar 
-xvf, then move to installers.
 >cd /usr/local/installers/primer3_0_9_test/src

I had to edit the Makefile using a hint from Alex Brown.
I removed the line:
LIBOPTS ='-static'
and then removed all references to $(LIBOPTS)

It has been suggested that you change CC=gcc to CC=CC, but I haven't.
 >make primer3
when finished, you can test
 >cd ../test
 >./primer_test.pl
Don't be totally dismayed if you see a FAILED during test after primer 
comparison.
if you ran the test, then
 >cd ../src
you need the primer3_core in the path of emboss, so copy it to 
emboss/bin
 >cp primer3_core /usr/local/emboss/bin
Seems to work for me from command line or Jemboss.  Let me know if this 
hack didn't cut it for you!

at this point it might be useful to build you locate database:
 >sudo /usr/libexec/locate.updatedb

Activating all the goodies:
you need to run:
aaextractindex, cutgextract, printsextract, prosextract, rebase
(there may be others that I ran, or other that I have yet to discover 
that I need to run).  I did this from commandline, but it looks like 
Jemboss will run them also.  Some of the target databases are in 
/usr/local/installers/EMBOSS-2.8.0/test/data, others have to be 
downloaded.  The appropriate source is on the corresponding help pages.




Current problems:
I have an display issue with .png files.  Plots and graphs made 
correctly, but they do not display properly in the results window.  If 
I save those displayed results, and open them in preview, they are 
fine; thus, it is a display issue only.

I hope this adequately thorough to provide some clues to any problems 
you are having with your install.

-Brett


––––––––––––––––––––––––––––––––––––––––––––––––––––––––
Brett Kaufman, Ph.D
3801 University
Rm 676
Montreal, QC H3A 2B4
Canada

brett.kaufman at mcgill.ca
(514) 398 8523
(514) 398 1509 (fax)
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